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In the 2140sdecade, Harris attained the rank of captain within Starfleet Security and eventually became the liaison officer to Starfleet Intelligence. Since SI was a fairly new organization at this time, it relied heavily on Security for its assets. Harris built around himself a group of trusted collegues and and occasional operatives. One such officer was EnsignMalcolm Reed. Since Harris's division operated in an administrative grey area, he was able to conduct missions and operations that weren't authorised by Starfleet, but Harris believed necessary for the security of Earth.

After years out of contact with Reed, Harris again contacted him in 2154. This time, Harris demanded that Reed stall an investigation into the abduction of DoctorPhlox, who Harris had kidnapped in order to help the Klingons cure the Qu'Vat virus. Reed reluctantly complied with Harris's directive, but CaptainJonathan Archer discovered the deception and forced Reed to put him in contact with Harris. Harris had in fact been working with Klingon AdmiralKrell the entire time because Harris thought it would benefit Earth by stabilizing the Klingon Empire. After the Enterprise foiled Harris and Krell's plans, Harris again contacted Reed, but Reed refused to listen to him. (ENTepisodes: "Divergence", "Affliction")

However, a month later, Harris would supply Reed with information about the baby that Terra Prime had created from the DNA of T'Pol and Charles Tucker III. Harris only supplied this information with Reed's promise that he would again follow Harris's orders. Later, Reed again asked Harris for help in penetrating the Mars detection grid to reach Terra Prime's base. (ENTepisodes: "Demons", "Terra Prime")

In 2164, he still worked for the agency and kept regular contact with Tucker. In that year, Harris dispatched him to Sauria in an attempt to find out what was really happening with the plague that started to spread on the planet months earlier, and to neutralize any future threats to the Federation. (ENT - Rise of the Federationnovel: Tower of Babel)

After Section 31 was exposed to the public in early 2166, Harris and his core agents made a run for it on a private ship to avoid capture. They intercepted Tucker's scout ship returning from Sauria and beamed him and his companion Devna aboard their ship. Harris admitted to Tucker that he compromised the Section by making too many mistakes too close together and, in order for the organization to survive it had to be reduced in size and lay low. To achive this, the agents overloaded the ship's reactor and commited suicide. (ENT - Rise of the Federationnovel: Patterns of Interference)